Is CDH10 p.Gly673= (c.2019C>T) pathogenic?

CDH10 p.Gly673= (c.2019C>T) is classified Benign in CDH10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-05-18). Rare (popmax 0.84%, nfe).

How common is CDH10 p.Gly673= (c.2019C>T) in the general population?

CDH10 p.Gly673= (c.2019C>T) is rare (popmax 0.84%, nfe) (gnomAD).

CDH10 p.Gly673=

c.2019C>T · rs141645081 · VCV772871

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.84%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.97	GERP 1.9, phastCons 1
Overall
CADD	7.362	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.84% European (non-Finnish) · 9,914/1,179,920 alleles

Filtering AF 0.826% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.821%

Overall 0.665% 10,724/1,613,838 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	6.03%	17
European (non-Finnish)grpmax	0.84%	119
Remaining individualsnot grpmax-eligible	0.467%	214
Ashkenazi Jewishnot grpmax-eligible	0.267%	375
Admixed American	0.252%	397
Finnishnot grpmax-eligible	0.172%	582
African / African-American	0.137%	728
Middle Eastern	0.099%	1,010
South Asian	0.0154%	6,504

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDH10
Protein: p.Gly673=
Coding: c.2019C>T
MANE Select: NM_006727
dbSNP: rs141645081
Type: single nucleotide variant
Location: chr5:24488011 (GRCh38)
Gene constraint: LOEUF 0.655 · pLI 0.18 (gnomAD)
Structure: AlphaFold pLDDT 78.29

Full CDH10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDH10 p.Met316Ile Uncertain significance ★★ ⚠ same type
CDH10 p.Thr159Met Uncertain significance ★★ ⚠ same type
CDH10 p.Glu469= Benign ★★ same type
CDH10 p.Ala296Thr Uncertain significance ★ ⚠ same type
CDH10 p.Ala501Val Uncertain significance ★ ⚠ same type
CDH10 p.Ala530Val Uncertain significance ★ ⚠ same type
CDH10 p.Arg128Cys Uncertain significance ★ ⚠ same type
CDH10 p.Arg268Cys Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdh10-p-gly673 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown